The effect of CreA in glucose and xylose catabolism in Aspergillus nidulans

CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner

Carbon catabolite repression enables fungi to utilize the most favourable carbon source in the environment, and is mediated by a key regulator, CreA, in most fungi. CreA-mediated regulation has mainly been studied at high monosaccharide concentrations, an uncommon situation in most natural biotopes. In nature, many fungi rely on plant biomass as their major carbon source by producing enzymes to degrade plant cell wall polysaccharides into metabolizable sugars. To determine the role of CreA when fungi grow in more natural conditions and in particular with respect to degradation and conversion of plant cell walls, we compared transcriptomes of a creA deletion and reference strain of the ascomycete Aspergillus niger during growth on sugar beet pulp and wheat bran. Transcriptomics, extracellular sugar concentrations and growth profiling of A. niger on a variety of carbon sources, revealed that also under conditions with low concentrations of free monosaccharides, CreA has a major effect on gene expression in a strong time and substrate composition dependent manner. In addition, we compared the CreA regulon from five fungi during their growth on crude plant biomass or cellulose. It showed that CreA commonly regulated genes related to carbon metabolism, sugar transport and plant cell wall degrading enzymes across different species. We therefore conclude that CreA has a crucial role for fungi also in adapting to low sugar concentrations as occurring in their natural biotopes, which is supported by the presence of CreA orthologs in nearly all fungi.

Regulating Strategies for Producing Carbohydrate Active Enzymes by Filamentous Fungal Cell Factories

Filamentous fungi are important eukaryotic organisms crucial in substrate degradation and carbon cycle on the earth and have been harnessed as cell factories for the production of proteins and other high value-added products in recent decades. As cell factories, filamentous fungi play a crucial role in industrial protein production as both native hosts and heterologous hosts. In this review, the regulation strategies of carbohydrate active enzyme expression at both transcription level and protein level are introduced, and the transcription regulations are highlighted with induction mechanism, signaling pathway, and promoter and transcription factor regulation. Afterward, the regulation strategies in protein level including suitable posttranslational modification, protein secretion enhancement, and protease reduction are also presented. Finally, the challenges and perspectives in this field are discussed. In this way, a comprehensive knowledge regarding carbohydrate active enzyme production regulation at both transcriptional and protein levels is provided with the particular goal of aiding in the practical application of filamentous fungi for industrial protein production.

Transcriptomic analysis of the oleaginous yeast Lipomyces starkeyi during lipid accumulation on enzymatically treated corn stover hydrolysate

BACKGROUND

Efficient and economically viable production of biofuels from lignocellulosic biomass is dependent on mechanical and chemical pretreatment and enzymatic hydrolysis of plant material. These processing steps yield simple sugars as well as plant-derived and process-added organic acids, sugar-derived dehydration products, aldehydes, phenolics and other compounds that inhibit the growth of many microorganisms. Lipomyces starkeyi is an oleaginous yeast capable of robust growth on a variety of sugars and lipid accumulation on pretreated lignocellulosic substrates making it attractive as an industrial producer of biofuels. Here, we examined gene expression during batch growth and lipid accumulation in a 20-L bioreactor with either a blend of pure glucose and xylose or pretreated corn stover (PCS) that had been enzymatically hydrolyzed as the carbon sources.

RESULTS

We monitored sugar and ammonium utilization as well as biomass accumulation and found that growth of L. starkeyi is inhibited with PCS hydrolysate as the carbon source. Both acetic acid and furfural are present at concentrations toxic to L. starkeyi in PCS hydrolysate. We quantified gene expression at seven time-points for each carbon source during batch growth and found that gene expression is similar at physiologically equivalent points. Analysis of promoter regions revealed that gene expression during the transition to lipid accumulation is regulated by carbon and nitrogen catabolite repression, regardless of carbon source and is associated with decreased expression of the translation machinery and suppression of the cell cycle. We identified 73 differentially expressed genes during growth phase in the bioreactor that may be involved in detoxification of corn stover hydrolysate.

CONCLUSIONS

Growth of L. starkeyi is inhibited by compounds present in PCS hydrolysate. Here, we monitored key metabolites to establish physiologically equivalent comparisons during a batch bioreactor run comparing PCS hydrolysate and purified sugars. L. starkeyi's response to PCS hydrolysate is primarily at the beginning of the run during growth phase when inhibitory compounds are presumably at their highest concentration and inducing the general detoxification response by L. starkeyi. Differentially expressed genes identified herein during growth phase will aid in the improvement of industrial strains capable of robust growth on substrates containing various growth inhibitory compounds.

Kinetic modeling of Stickland reactions-coupled methanogenesis for a methanogenic culture

Studying amino acid catabolism-coupled methanogenesis is the important standpoints to decipher the metabolic behavior of a methanogenic culture. l-Glycine and l-alanine are acted as sole carbon and nitrogen sources for acidogenic bacteria. One amino acid is oxidized and another one is reduced for acetate production via pyruvate by oxidative deamination process in the Stickland reactions. Herein, we have developed a kinetic model for the Stickland reactions-coupled methanogenesis (SRCM) and simulated objectively to maximize the rate of methane production. We collected the metabolic information from enzyme kinetic parameters for amino acid catabolism of Clostridium acetobutylicum ATCC 824 and methanogenesis of Methanosarcina acetivorans C2A. The SRCM model of this study consisted of 18 reactions and 61 metabolites with enzyme kinetic parameters derived experimental data. The internal or external metabolic flux rate of this system found to control the acidogenesis and methanogenesis in a methanogenic culture. Using the SRCM model, flux distributions were calculated for each reaction and metabolite in order to maximize the methane production rate from the glycine–alanine pair. Results of this study, we demonstrated the metabolic behavior, metabolite pairing while mutually interact, and advantages of syntrophic metabolism of amino acid-directed methane production in a methanogenic starter culture.

Modulating Transcriptional Regulation of Plant Biomass Degrading Enzyme Networks for Rational Design of Industrial Fungal Strains

Filamentous fungi are the most important microorganisms for the industrial production of plant polysaccharide degrading enzymes due to their unique ability to secrete these proteins efficiently. These carbohydrate active enzymes (CAZymes) are utilized industrially for the hydrolysis of plant biomass for the subsequent production of biofuels and high-value biochemicals. The expression of the genes encoding plant biomass degrading enzymes is tightly controlled. Naturally, large amounts of CAZymes are produced and secreted only in the presence of the plant polysaccharide they specifically act on. The signal to produce is conveyed via so-called inducer molecules which are di- or mono-saccharides (or derivatives thereof) released from the specific plant polysaccharides. The presence of the inducer results in the activation of a substrate-specific transcription factor (TF), which is required not only for the controlled expression of the genes encoding the CAZymes, but often also for the regulation of the expression of the genes encoding sugar transporters and catabolic pathway enzymes needed to utilize the released monosaccharide. Over the years, several substrate-specific TFs involved in the degradation of cellulose, hemicellulose, pectin, starch and inulin have been identified in several fungal species and systems biology approaches have made it possible to uncover the enzyme networks controlled by these TFs. The requirement for specific inducers for TF activation and subsequently the expression of particular enzyme networks determines the choice of feedstock to produce enzyme cocktails for industrial use. It also results in batch-to-batch variation in the composition and amounts of enzymes due to variations in sugar composition and polysaccharide decorations of the feedstock which hampers the use of cheap feedstocks for constant quality of enzyme cocktails. It is therefore of industrial interest to produce specific enzyme cocktails constitutively and independently of inducers. In this review, we focus on the methods to modulate TF activities for inducer-independent production of CAZymes and highlight various approaches that are used to construct strains displaying constitutive expression of plant biomass degrading enzyme networks. These approaches and combinations thereof are also used to construct strains displaying increased expression of CAZymes under inducing conditions, and make it possible to design strains in which different enzyme mixtures are simultaneously produced independently of the carbon source.

The fungus Aspergillus niger consumes sugars in a sequential manner that is not mediated by the carbon catabolite repressor CreA

In nature, the fungus Aspergillus niger degrades plant biomass polysaccharides to monomeric sugars, transports them into its cells, and uses catabolic pathways to convert them into biochemical building blocks and energy. We show that when grown in liquid cultures, A. niger takes up plant-biomass derived sugars in a largely sequential manner. Interestingly, this sequential uptake was not mediated by the fungal general carbon catabolite repressor protein CreA. Furthermore, transcriptome analysis strongly indicated that the preferential use of the monomeric sugars is arranged at the level of transport, but it is not reflected in transcriptional regulation of sugar catabolism. Therefore, the results indicate that the regulation of sugar transport and catabolism are separate processes in A. niger.

The ACEII recombinant Trichoderma reesei QM9414 strains with enhanced xylanase production and its applications in production of xylitol from tree barks

Background

ACEII transcription factor plays a significant role in regulating the expression of cellulase and hemicellulase encoding genes. Apart from ACEII, transcription factors such as XYR1, CRE1, HAP2/3/5 complex and ACEI function in a coordinated pattern for regulating the gene expression of cellulases and hemicellulases. Studies have demonstrated that ACEII gene deletion results in decreased total cellulase and xylanase activities with reduced transcript levels of lignocellulolytic enzymes.

Results

In this study, we have successfully transformed the ACEII transcription factor encoding gene in Trichoderma reesei to significantly improve its degrading abilities. Transformation experiments on parental strain T. reesei QM9414 has resulted in five genetically engineered strains T/Ace2-2, T/Ace2-5, T/Ace2-8, T/Ace5-4 and T/Ace10-1. Among which, T/Ace2-2 has exhibited significant increase in enzyme activity by twofolds, when compared to parental strain. The T/Ace2-2 was cultured on growth substrates containing 2% bark supplemented with (a) sugar free + MA medium (b) glucose + MA medium and (c) xylose + MA medium. The bark degradation efficiency of genetically modified T/Ace2-2 strain was assessed by analyzing the xylitol production yield using HPAEC. By 6th day, about 10.52 g/l of xylitol was produced through enzymatic conversion of bark (2% bark + MA + xylose) by the T/Ace2-2 strain and by 7th day the conversion rate was found to be 0.21 g/g. Obtained results confirmed that bark growth medium supplemented with d-xylose has profoundly increased the conversion rate of bark by T/Ace2-2 strain when compared to sugar free and glucose supplemented growth media. Results obtained from scanning electron microscopy has endorsed our current results. Bark samples inoculated with T/Ace2-2 strain has showed large number of degraded cells with clearly visible cavities and fractures, by exposing the microfibrillar interwoven complex.

Conclusion

We propose a cost effective and ecofriendly method for the degradation of lignocellulosic biomass such as bark to produce xylitol by using genetically modified T. reesei. Efficient conversion rate and production yield obtained in our current study provides a great scope for the xylitol industries, as our method bypasses the pretreatment of bark achieving clean and low-cost xylitol production.

Molecular cloning and comparative sequence analysis of fungal β-Xylosidases

Commercial scale degradation of hemicelluloses into easily accessible sugar residues is practically crucial in industrial as well as biochemical processes. Xylanolytic enzymes have a great number of possible applications in many biotechnological processes and therefore, these enzymes are continuously attracting the attention of scientists. Due to this fact, different β-Xylosidases have been isolated, purified and characterized from several bacteria and fungi. Microorganisms in this respect have gained much momentum for production of these significant biocatalysts with remarkable features. It is difficult to propagate microorganisms for efficient and cost-competitive production of β-Xylosidase from hemicelluloses due to expensive conditions of fermentation. The screening of new organisms with an enhanced production of β-Xylosidases has been made possible with the help of recombinant DNA technology. β-Xylosidase genes haven been cloned and expressed on large scale in both homologous and heterologous hosts with the advent of genetic engineering. Therefore, we have reviewed the literature regarding cloning of β-Xylosidase genes into various hosts for their heterologous production along with sequence similarities among different β-Xylosidases. The study provides insight into the current status of cloning, expression and sequence analysis of β-Xylosidases for industrial applications.

Genome-wide transcriptomic analysis of a superior biomass-degrading strain of A. fumigatus revealed active lignocellulose-degrading genes

Background

Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural materials on earth. It consists of complex carbohydrates and aromatic polymers found in the plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was isolated from compost heaps and showed highly efficient plant biomass-degradation capability.

Results

The 29-million base-pair genome of Z5 was sequenced and 9540 protein-coding genes were predicted and annotated. Genome analysis revealed an impressive array of genes encoding cellulases, hemicellulases and pectinases involved in lignocellulosic biomass degradation. Transcriptional responses of A. fumigatus Z5 induced by sucrose, oat spelt xylan, Avicel PH-101 and rice straw were compared. There were 444, 1711 and 1386 significantly differently expressed genes in xylan, cellulose and rice straw, respectively, when compared to sucrose as a control condition.

Conclusions

Combined analysis of the genomic and transcriptomic data provides a comprehensive understanding of the responding mechanisms to the most abundant natural polysaccharides in A. fumigatus. This study provides a basis for further analysis of genes shown to be highly induced in the presence of polysaccharide substrates and also the information which could prove useful for biomass degradation and heterologous protein expression.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1658-2) contains supplementary material, which is available to authorized users.

Xylitol production by genetically engineered Trichoderma reesei strains using barley straw as feedstock

Xylitol, a naturally occurring five-carbon sugar alcohol derived from D-xylose, is currently in high demand by industries. Trichoderma reesei, a prolific industrial cellulase and hemicellulase producing fungus, is able to selectively use D-xylose from hemicelluloses for xylitol production. The xylitol production by T. reesei can be enhanced by genetic engineering of blocking further xylitol metabolism in the D-xylose pathway. We have used two different T. reesei strains which are impaired in the further metabolism of xylitol including a single mutant in which the xylitol dehydrogenase gene was deleted (∆xdh1) and a double mutant where additionally L-arabinitol-4-dehydrogenase, an enzyme which can partially compensate for xylitol dehydrogenase function, was deleted (∆lad1∆xdh1). Barely straw was first pretreated using NaOH and Organosolv pretreatment methods. The highest xylitol production of 6.1 and 13.22 g/L was obtained using medium supplemented with 2 % Organosolv-pretreated barley straw and 2 % D-xylose by the ∆xdh1 and ∆lad1∆xdh1 strains, respectively.

Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing

A key challenge in the production of second generation biofuels is the conversion of lignocellulosic substrates into fermentable sugars. Enzymes, particularly those from fungi, are a central part of this process, and many have been isolated and characterised. However, relatively little is known of how fungi respond to lignocellulose and produce the enzymes necessary for dis-assembly of plant biomass. We studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA sequencing we showed that, 24 hours after exposure to straw, gene expression of known and presumptive plant cell wall-degrading enzymes represents a huge investment for the cells (about 20% of the total mRNA). Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal arsenal of enzymes for the degradation of plant biomass. Using transcription factor deletion mutants (xlnR and creA) to study the response to both lignocellulosic substrates and low carbon source concentrations, we showed that a subset of genes coding for degradative enzymes is induced by starvation. Our data support a model whereby this subset of enzymes plays a scouting role under starvation conditions, testing for available complex polysaccharides and liberating inducing sugars, that triggers the subsequent induction of the majority of hydrolases. We also showed that antisense transcripts are abundant and that their expression can be regulated by growth conditions.

Differential regulation of the cellulase transcription factors XYR1, ACE2, and ACE1 in Trichoderma reesei strains producing high and low levels of cellulase

Due to its capacity to produce large amounts of cellulases, Trichoderma reesei is increasingly being investigated for second-generation biofuel production from lignocellulosic biomass. The induction mechanisms of T. reesei cellulases have been described recently, but the regulation of the genes involved in their transcription has not been studied thoroughly. Here we report the regulation of expression of the two activator genes xyr1 and ace2, and the corepressor gene ace1, during the induction of cellulase biosynthesis by the inducer lactose in T. reesei QM 9414, a strain producing low levels of cellulase (low producer). We show that all three genes are induced by lactose. xyr1 was also induced by d-galactose, but this induction was independent of d-galactose metabolism. Moreover, ace1 was carbon catabolite repressed, whereas full induction of xyr1 and ace2 in fact required CRE1. Significant differences in these regulatory patterns were observed in the high-producer strain RUT C30 and the hyperproducer strain T. reesei CL847. These observations suggest that a strongly elevated basal transcription level of xyr1 and reduced upregulation of ace1 by lactose may have been important for generating the hyperproducer strain and that thus, these genes are major control elements of cellulase production.

D-Xylose as a repressor or inducer of xylanase expression in Hypocrea jecorina (Trichoderma reesei)

For Hypocrea jecorina (anamorph Trichoderma reesei), a filamentous fungus used for hydrolase production in different industries, it has been a long-term practice to use d-xylose as an inducing substance. We demonstrate in this study that the degree of xylanase-encoding gene induction strictly depends on the concentration of d-xylose, which was found to be optimal from 0.5 to 1 mM for 3 h of cultivation. At higher concentrations of d-xylose, a reduced level of xylanase gene expression was observed. In the present study, we also provide evidence that the d-xylose concentration-dependent induction is antagonized by carbon catabolite repressor 1. This repressor mediates its influence on d-xylose indirectly, by reducing the expression of xylanase regulator 1, the main activator of most hydrolase-encoding genes. Additionally, a direct influence of the repressor on xylanase 1 expression in the presence of d-xylose was found. Furthermore, we show that d-xylose reductase 1 is needed to metabolize d-xylose to achieve full induction of xylanase expression. Finally, a strain which expresses xylanase regulator 1 at a constant level was used to partially overcome the negative influence exerted by carbon catabolite repressor 1 on d-xylose.

Physiological characterisation of acuB deletion in Aspergillus niger

The acuB gene of Aspergillus niger is an ortholog of facB in Aspergillus nidulans. Under carbon-repression conditions, facB is repressed, thereby preventing acetate metabolism when the repressing carbon source is present. Even though facB is reported to be repressed directly by CreA, it is believed that a basal level of FacB activity exists under glucose-repressive conditions. In the present study, the effect of deletion of acuB on the physiology of A. niger was assessed. Differences in organic acid and acetate production, enzyme activities and extracellular amino and non-amino organic acid production were determined under glucose-repressing and -derepressing conditions. Furthermore, consumption of alternative carbon sources (e.g. xylose, citrate, lactate and succinate) was investigated. It was shown that AcuB has pleiotropic effects on the physiology of A. niger. The results indicate that metabolic pathways that are not directly involved in acetate metabolism are influenced by acuB deletion. Clear differences in organic acid consumption and production were detected between the acuB and reference strain. However, the hypothesis that AcuB is responsible for basal AcuA activity necessary for activation of acetate metabolic pathways, even during growth on glucose, could not be confirmed. The experiments demonstrated that also when acuB was deleted, no acetate was formed. Therefore, AcuB cannot be the only activator of AcuA, and another control mechanism has to be available for activating AcuA.

CreA mediates repression of the regulatory gene xlnR which controls the production of xylanolytic enzymes in Aspergillus nidulans

The Aspergillus nidulans xlnR gene encodes a Zn(2)Cys(6) transcription activator necessary for the synthesis of the main xylanolytic enzymes, i.e. endo-xylanases X(22), X(24) and X(34), and beta-xilosidase XlnD. Expression of xlnR is not sufficient for induction of genes encoding the xylanolytic complex, the presence of xylose is absolutely required. It has been established previously that the wide-domain carbon catabolite repressor CreA indirectly represses xlnA (encodes X(22)) and xlnB (encodes X(24)) genes as well as exerting direct repression on xlnA. This work provides evidence that CreA-mediated indirect repression occurs through repression of xlnR: (i) the xlnR gene promoter is repressed by glucose and this repression is abolished in creA(d)30 mutant strains and (ii) deregulated expression of xlnR completely relieves glucose repression of xlnA and xlnB. Thus, CreA and XlnR form a transcriptional cascade regulating A. nidulans xylanolytic genes.

Regulation of xylanase in Aspergillus phoenicis: a physiological and molecular approach

Microbial xylanolytic enzymes have a promising biotechnological potential, and are extensively applied in industries. In this study, induction of xylanolytic activity was examined in Aspergillus phoenicis. Xylanase activity induced by xylan, xylose or beta-methylxyloside was predominantly extracellular (93-97%). Addition of 1% glucose to media supplemented with xylan or xylose repressed xylanase production. Glucose repression was alleviated by addition of cAMP or dibutyryl-cAMP. These physiological observations were supported by a Northern analysis using part of the xylanase gene ApXLN as a probe. Gene transcription was shown to be induced by xylan, xylose, and beta-methylxyloside, and was repressed by the addition of 1% glucose. Glucose repression was partially relieved by addition of cAMP or dibutyryl cAMP.

Physiological characterization of xylose metabolism inAspergillus niger under oxygen-limited conditions

The physiology of Aspergillus niger was studied under different aeration conditions. Five different aeration rates were investigated in batch cultivations of A. niger grown on xylose. Biomass, intra- and extra-cellular metabolites profiles were determined and ten different enzyme activities in the central carbon metabolism were assessed. The focus was on organic acid production with a special interest in succinate production. The fermentations revealed that oxygen limitation significantly changes the physiology of the micro-organism. Changes in extra cellular metabolite profiles were observed, that is, there was a drastic increase in polyol production (erythritol, xylitol, glycerol, arabitol, and mannitol) and to a lesser extent in the production of reduced acids (malate and succinate). The intracellular metabolite profiles indicated changes in fluxes, since several primary metabolites, like the intermediates of the TCA cycle accumulated during oxygen limitation (on average three fold increase). Also the enzyme activities showed changes between the exponential growth phase and the oxygen limitation phase. In general, the oxygen availability has a significant impact on the physiology of this fungus causing dramatic alterations in the central carbon metabolism that should be taken into account in the design of A. niger as a succinate cell factory.

CreA influences the metabolic fluxes of Aspergillus nidulans during growth on glucose and xylose

The physiological phenotype of Aspergillus nidulans was investigated for different genetic and environmental conditions of glucose repression through the quantification of in vivo fluxes in the central carbon metabolism using (13)C-metabolic-flux analysis. The particular focus was the role of the carbon repressor CreA, which is the major regulatory protein mediating carbon repression in many fungal species, in the primary metabolism of A. nidulans. Batch cultivations were performed with a reference strain and a deletion mutant strain (creADelta4) using [1-(13)C]glucose as carbon source. The mutant strain was also grown on a mixture of [1-(13)C]glucose and unlabelled xylose. Fractional enrichment data were measured by gas chromatography-mass spectrometry. A model describing the central metabolism of A. nidulans was used in combination with fractional enrichment data, and measurements of extracellular rates and biomass composition for the estimation of the in vivo metabolic fluxes. The creA-mutant strain showed a lower maximum specific growth rate than the reference strain when grown on glucose (0.11 and 0.25 h(-1), respectively), whereas the specific growth rate of the mutant strain grown on the glucose/xylose mixture was identical to that on glucose (0.11 h(-1)). Different patterns and increased levels of extracellular polyols were observed both upon deletion of the creA gene and upon addition of xylose to the growth medium of the mutant strain. Concerning metabolic fluxes, the major change observed in the flux distribution of A. nidulans upon deletion of the creA gene was a 20 % decrease in the flux through the oxidative part of the pentose-phosphate pathway. Addition of xylose to the growth medium of the mutant resulted in an increase of about 40 % in the activity of the oxidative part of the pentose-phosphate pathway, as well as decreases in the fluxes through the Embden-Meyerhof-Parnas pathway and the tricarboxylic acid cycle (in the range of 20-30 %). The derepression of key pathways leads to alterations in the demands for cofactors, thereby imposing changes in the central metabolism due to the coupling of the many different reactions via the redox and energy metabolism of the cells.